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Yorodumi- PDB-6yk9: [Fe]-hydrogenase from Methanolacinia paynteri with bound guanylyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yk9 | ||||||||||||
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Title | [Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A resolution | ||||||||||||
Components | 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||||||||
Keywords | OXIDOREDUCTASE / [Fe]-hydrogenase / FeGP cofactor / guanylylpyridinol / conformational changes / GMP | ||||||||||||
Function / homology | GUANOSINE-5'-MONOPHOSPHATE / Chem-FEG / GLYCINE / GUANOSINE Function and homology information | ||||||||||||
Biological species | Methanolacinia paynteri G-2000 (archaea) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||||||||
Authors | Wagner, T. / Huang, G. / Arriaza-Gallardo, F.J. / Shima, S. | ||||||||||||
Funding support | Germany, China, 3items
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Citation | Journal: J.Mol.Biol. / Year: 2020 Title: The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. Authors: Huang, G. / Wagner, T. / Demmer, U. / Warkentin, E. / Ermler, U. / Shima, S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yk9.cif.gz | 543.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yk9.ent.gz | 445.2 KB | Display | PDB format |
PDBx/mmJSON format | 6yk9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yk9_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6yk9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6yk9_validation.xml.gz | 57.3 KB | Display | |
Data in CIF | 6yk9_validation.cif.gz | 85.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yk/6yk9 ftp://data.pdbj.org/pub/pdb/validation_reports/yk/6yk9 | HTTPS FTP |
-Related structure data
Related structure data | 6tgeC 6tlkC 6tm3C 6ykaC 6ykbC 4jjfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCE
#1: Protein | Mass: 37223.199 Da / Num. of mol.: 4 / Mutation: Wild-type Source method: isolated from a genetically manipulated source Details: / Source: (gene. exp.) Methanolacinia paynteri G-2000 (archaea) Tissue: / / Cell: / / Cell line: / / Gene: hmd / Organ: / / Variant: DSM 2545 Details (production host): The DNA synthesized was inserted into the expression vector pET-24b (+) at the NdeI and SalI restriction-enzyme digestion-sites Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / References: 5,10-methenyltetrahydromethanopterin hydrogenase |
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-Non-polymers , 6 types, 1075 molecules
#2: Chemical | ChemComp-FEG / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Chemical | #6: Chemical | ChemComp-GMP / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.42 % / Description: Transparent long orthorhombic rod |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 at 283.15 K using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of ...Details: [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 at 283.15 K using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution (from crystallization kits) under yellow light and incubated under dark conditions. The best diffracting crystal came out within two weeks in 25% w/v polyethylene glycol 1500 and 100 mM SPG buffer pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience). For cryo protection, the crystal was soaked in the crystallization solution supplemented with 10% v/v glycerol. PH range: 8.5 / Temp details: / |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→82.92 Å / Num. obs: 133035 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.76 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.065 / Rrim(I) all: 0.125 / Rsym value: 0.107 / Net I/av σ(I): 5.4 / Net I/σ(I): 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JJF Resolution: 1.7→24.89 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.912 / SU R Cruickshank DPI: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.122 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.109
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Displacement parameters | Biso max: 115.74 Å2 / Biso mean: 23.15 Å2 / Biso min: 6.61 Å2
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Refine analyze | Luzzati coordinate error obs: 0.24 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→24.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.74 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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